Genome biology of rust fungi and applications for biosecurity

Abstract

Fungal plant pathogens of the order Pucciniales can cause rust disease on a diverse range of host species, including economically and ecologically important crops and trees. Rust fungi are dikaryotic, maintaining two nuclei per cell throughout most of their life cycle. Urediniospores in the asexual life cycle of rust fungi have high mobility, can easily spread via wind or water, readily infect their host and cause epidemics. The sexual part of the life-cycle provides opportunities for recombination and genetic reassortment generating new virulence combinations. Due to their dikaryotic genome organisation rusts can also exchange nuclei by somatic hybridization asexually, which can also result in the emergence of new virulent strains. Whether two nuclei are compatible are hypothesized to be determined by two permanently heterozygous mating type (MAT) loci: the homeodomain transcription factor (HD) locus and the pheromone receptor (PR) locus. Hence, understanding mating compatibility can help predict possible emergence of new virulent isolates. The genome biology and structure of the MAT locus in rust fungi is unclear since mating compatibility determining loci are often repeat-rich, which makes them difficult to assemble. Now, with high-quality genome assemblies of cereal rust fungi available, this thesis provides detailed insight into the MAT loci of rust fungi. Most rust fungal pathogens such as cereal rust fungi, are highly host-specific, whereas Austropuccinia psidii, the myrtle rust pathogen, has a broad host range and threatens many plants in the Myrtaceae family. The pathogenicity of A. psidii varies among biotypes, with different biotypes displaying different host specificity and aggressiveness. The pandemic biotype has spread globally, including to Australia, causing substantial ecosystem damage. While only the pandemic biotype has been reported in Australia, the introduction of other exotic strains poses a threat of even greater damage to Australian forests. To better understand the genome biology of A. psidii and to develop improved diagnostic tools, a high-quality reference genome is essential. This thesis aims to investigate the genome biology of rust fungi and extend to application in biosecurity via three main objectives: (i) comparative analysis of MAT loci among cereal rust fungi, (ii) generate and investigate haplotype-phased chromosome-scale genome assembly of A. psidii, (iii) develop diagnostic markers to distinguish A. psidii biotypes to improve Australian biosecurity measures. From comparison of MAT loci among four economically important rust species, the research provided insight into the evolutionary history of MAT loci in these species. Understanding mating compatibility can help predict potential emergence of new virulent isolates of these plant pathogens. The high-quality genome assembly of A. psidii served as a fundamental resource for the genome studies and for candidate effector identification. Besides, the high-quality reference genome enabled the design of sensitive markers that allow for the differentiation of different A. psidii biotypes in a biosecurity setting. Show more